It's already in the works, but OrbiterSound is tied to the new release of Orbiter itself. So we all have to wait.
What you described is a known issue, there is basically no way around it, some addons might even not work at all.
You will also notice that certain sounds are mixed up. Like the Vespucci's reactor sound that might sound like the
DG3's airlock opening

What you can do is put the vessel who's sounds you would prefer to "dominate" Orbiter as the last entry in the .scn
file. Its sounds will then take precedence over the ships listed before it. Imagine a layered cake. The topmost layer is
the one, you see whole, the rest you only see in those parts, where the previous layers don't cover them. Same
thing in OrbiterSound. The sound slots are loaded one on top of eachother and the last ship gets to overlap all the
rest, depending on how many sounds it itself uses.
The new OS will have 60 sounds per vessel and no more mixing up of sounds.
Cheers,